[Dana Newell] "I think the problem was that Final cut doesn't recognise 'True HD' files. It seemed to be flipping out with the sizes."
FC has no problem to manage any size.
1440x1080 HD pixels is mostly an acquistion size (HDV, DVCPRoHD) and unless you need to deliver with those specs you shouldn't finish in that size.
Standar HD has only two sizes 1920x1080 and 1280x720. Always Squared pixels.
Probably FC was setting the sequence size 1920x1080 which is TRUE HD.
I don't know where you wan't to end up but if you are working for a web video, you shouldn't use that size/pixels, neither work in an Interlaced sequence.
[Dana Newell] "used Animation Pixlet Pal to export out."
That's codec that nobody knows what is for.
I've never heard of nobody using it for nothing.
http://en.wikipedia.org/wiki/Pixlet
rafael
http://www.nagavideo.com